With the implementation of GATK for variant call, it was suggested as “better practice” by Broad Institute to include “base calling score recalibration”. Here is what has been done in the past
Getting the set up for both dscr and lsrc.
At dscr
1. Script: /home/chavi/jl407/GATK-testing/workingDir/GATK_recal.pl & /home/chavi/jl407/GATK-testing/workingDir/Global.pm
2. Sample command:
qsub /home/chavi/jl407/GATK-testing/workingDir/GATK_recal.pl
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/combined/combined_rmdup.bam
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/b57mod030_precal.csv
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/combined/combined_recal.bam
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/b57mod030_recal.csv
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/
/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod030/GATK/
At lsrc